I don't think Joss is unaware of the shippers. But I don't think shipping interests him, and I don't think he cares who Buffy ends up with - I think he'd be perfectly happy for her to end up with no one.

But on the other hand, I think he's perfectly aware that shipping sells. So the most logical course for him to pursue is to string the shippers of all camps along for as long as possible without committing to anything.